Publications
M. E. Wall. In press. Methods and software for diffuse X-ray scattering from protein crystals. Methods in Molecular Biology.
D. W. Dreisigmeyer, J. Stajic, I. Nemenman, W. S. Hlavacek, M. E. Wall. Determinants of bistability in induction of the Escherichia coli lac operon. IET Systems Biology. In press. Preprint (pdf).
R. G. Martin, E. S. Bartlett, J. L. Rosner, M. E. Wall. 2008. Activation of the Escherichia coli marA/soxS/rob regulon in response to transcriptional activator concentration. J Mol Biol 380:278-284. (PubMed).
D. Ming, J. D. Cohn, M. E. Wall. 2008. Fast dynamics perturbation analysis for prediction of protein functional sites. BMC Structural Biology 8:5. (PubMed; URL).
D. Ming, M. Anghel, M. E. Wall. 2007. Hidden structure in protein energy landscapes. Phys. Rev. E. 77:021902. (PubMed). Preprint (pdf).
J. S. Edwards, J. R. Faeder, W. S. Hlavacek, Y. Jiang, I. Nemenman, M. E. Wall. 2007. q-bio 2007: a watershed moment in modern biology. Mol Syst Biol 3:148 (PubMed; URL)
I. Nemenman, G. S. Escola, W. S. Hlavacek, P. J. Unkefer, C. J. Unkefer, M. E. Wall. 2007. Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism. Ann NY Acad Sci 1115:102-115 (pdf; arXiv:0706.2007).
D. Ming, M. E. Wall, K. Y. Sanbonmatsu. 2007. Domain motions of Argonaute, the catalytic engine of RNA interference. BMC Bioinformatics 8:470 (PubMed; URL)
M. E. Wall. 2006. Ligand Binding, Protein Fluctuations, and Allosteric Free Energy. AIP Conference Proceedings 851:16-33. Preprint (pdf). arXiv (q-bio.BM/0603027).
D. Ming, M. E. Wall. 2006. Interactions in native binding sites cause a large change in protein dynamics. J Mol Biol 358:213-223. Reprint (pdf). Preprint (pdf).
D. Ming, M. E. Wall. 2005. Allostery in a Coarse-Grained Model of Protein Dynamics. Phys Rev Lett 95:198301. Reprint (URL). Preprint (pdf). arXiv (q-bio.BM/0506031).
M.E. Wall, M.J. Dunlop, W.S. Hlavacek. 2005. Multiple functions of a feed-forward-loop gene circuit. J Mol Biol 349:501-514. Reprint (URL); Preprint (pdf).
M.J. Dunlop, M.E. Wall. 2005. Robustness in Gene Circuits: Clustering of Functional Responses. Proceedings of the 2005 American Control Conference 6:4411-4416. Preprint (q-bio.MN/0503005).
D. Ming, M.E. Wall. 2005. Quantifying Allosteric Effects in Proteins. Proteins 59:697-707. Preprint (pdf). Early View (html).
M.E. Wall, W.S. Hlavacek, M.A. Savageau.
2004. Design of gene circuits: lessons from bacteria. Nat Rev Genet 5:34-42. Reprint (pdf); Online table (pdf); EcoTFs web site (URL).
M.E. Wall, W.S. Hlavacek, M.A. Savageau. 2003.
Design principles for regulator gene expression in a repressible gene
circuit. J Mol Biol 332:861-876. (PubMed;pdf preprint)
M.E. Wall, S.H.
Francis, J.D. Corbin, K. Grimes, R. Richie-Jannetta, J. Kotera, B.A.
Macdonald, R.R. Gibson, J. Trewhella. 2003. Mechanisms associated with
cGMP binding and activation of cGMP-dependent protein kinase. Proc
Natl Acad Sci USA 100:2380-2385. (PubMed) M.E. Wall, A.
Rechtsteiner, L.M. Rocha. 2003. Singular Value Decomposition and
Principal Component Analysis. In A Practical Approach to
Microarray Data Analysis. D.P. Berrar, W. Dubitzky, M. Granzow,
eds. pp. 91-109, Kluwer:Norwell, MA. (pdf; html) M.E. Wall, P.A.
Dyck, T.S. Brettin. 2001. SVDMAN – singular value decomposition
analysis of microarray data. Bioinformatics 6:566-568. (PubMed) M.E. Wall, S.C.
Gallagher, J. Trewhella. 2000. Large-scale shape changes in proteins
and macromolecular complexes. Ann Rev Phys Chem 51:355-380. (PubMed) C.S. Tung, M.E.
Wall, S.C. Gallagher and J. Trewhella. 2000. A model of troponin-I in
complex with troponin-C using hybrid experimental data: the inhibitory
region is a b-hairpin. Protein Sci
7:1312-1326 (cover article)(PubMed) M.E. Wall, S.
Subramaniam and G.N. Phillips, Jr. 1999. Protein structure
determination using a database of interatomic distance probabilities. Protein
Sci 8:2720-2727. (PubMed) M.E. Wall, J.B.
Clarage and G.N. Phillips, Jr. 1997. Motions of calmodulin
characterized using both Bragg and diffuse X-ray scattering. Structure
5:1599-1612. (
PubMed) M.E. Wall, S.E.
Ealick and S.M. Gruner. 1997. Three-dimensional diffuse X-ray
scattering from crystals of Staphylococcal nuclease. Proc Natl Acad
Sci USA 94:6180-6184. (PubMed) R.L. Walter, D.J.
Thiel, S.L. Barna, M.W. Tate, M.E. Wall, E.F. Eikenberry, S.M. Gruner
and S.E. Ealick. 1995. High-resolution macromolecular structure
determination using CCD detectors and synchrotron radiation. Structure
3:835. (PubMed) M.W. Tate, E.F.
Eikenberry, S.L. Barna, M.E. Wall, J.L. Lowrance and S.M. Gruner. 1995.
A large-format high-resolution area X-ray detector based on a
fiber-optically bonded charge-coupled device (CCD). J Appl Cryst
28:196. (PubMed) S.M. Gruner, S.L.
Barna, M.E. Wall, M.W. Tate and E.F. Eikenberry. 1993. Characterization
of polycrystalline phosphors for area X-ray detectors. SPIE Vol.
2009 X-ray Detector Physics and Applications II, 98. (SPIE) Publications (abstracts 2003 and earlier) M.E. Wall, W.S. Hlavacek, M.A. Savageau. BISTI symposium 2003,
NIH, Bethesda, MD. Digital Biology: The Emerging Paradigm.
11/6/2003-11/7/2003. Poster: Design Principles for a Represible Gene
Circuit. A. Rechtsteiner, R. Gottardo, M.E. Wall & L.M. Rocha. RECOMB
2003 meeting, 4/10/2003-4/13/2003, Berlin. Poster: SINGULAR VALUE
DECOMPOSITION AND DENSITY ESTIMATION FOR FILTERING AND ANALYSIS OF GENE
EXPRESSION M.E. Wall, W.S. Hlavacek, M.A. Savageau. Keystone Symposium on
Functional Genomics: Global Analysis of Complex Biological Systems,
2/20/2003-2/25/2003, Santa Fe. Poster: Design principles of repressible
gene circuits. M.E. Wall, S.H.
Francis, J. Trewhella. 2002. Mechanisms associated with cGMP binding
and activation of cGMP-dependent protein kinase. Proceedings of
the Third International Conference on Systems Biology, E. Aurell,
J. Elf, J. Jeppsson, eds., p. 220. M.E. Wall, W.S.
Hlavacek, M.A. Savageau. 2002. Design principles for repressiple gene
circuits. Proceedings of the Third International Conference on
Systems Biology, E. Aurell, J. Elf, J. Jeppsson, eds., p. 221. A. Evangelisti,
W. S. Hlavacek, J. Ambrosiano, M. Wall, D. Sharp, J. M. Ettinger, D.
Hill. 2001. Methods for inference of genetic regulatory networks. Proceedings
of the Second International Conference on Systems Biology, T-M. Yi,
M. Hucka, M. Morohashi, H. Kitano, eds., p. 75. D. Hill, W.
Hlavacek, J. Ambrosiano, M. E. Wall, D. H. Sharp, T. Cleland, S. M.
Mniszewski, A. Evangelisti. 2001. Integrated clustering and motif
detection for genome-wide expression and sequence data. Proceedings
of the Second International Conference on Systems Biology, T-M. Yi,
M. Hucka, M. Morohashi, H. Kitano, eds., p. 83. P. Dyck, M.
Wall, T. Brettin. 2000. Validation of singular value decomposition
of global expression data. J. Comp. Biol. 7:636 C.S. Tung, M.E.
Wall, S.C. Gallagher and J. Trewhella. 2000. A molecular model of
the troponin-C/troponin-I interaction using constraints from NMR,
crystallography, small-angle scattering, cross-linking and FRET. Biophys.
J. 78(2) M.E. Wall,
G.N. Phillips, M. Stupar and S. Subramaniam. 1998. Refinement of X-ray
structures using a database of pairwise atomic distance probabilities. Biophys.
J. 74(2):A132 M.E. Wall
and G.N. Phillips, Jr. 1997. Motions of crystalline calmodulin studied
by multiple-conformer refinement and diffuse X-ray scattering. Biophys.
J. 72(2):A106 M.E. Wall,
S.M. Gruner and S. Ealick. 1996. Three-dimensional maps of diffuse
X-ray scattering from Staphylococcal nuclease. Biophys. J.
70(2):A60 J.T. Gleeson,
M.E. Wall, S. Erramilli and S.M. Gruner. 1993. Freezing and melting of
ice in lamellar lipid-water dispersions. Biophys. J.
64(2):A295 M.E. Wall
and E. Shyamsunder. 1992. Microwave dielectric response of heme protein
solutions as a function of temperature. Biophys. J. 61(2):A56 Presentations (2003 and earlier) MIPNETS workshop on Proteins and Signals, 6/25/2003, Liverpool,
UK. Invited talk: Mechanisms of Biochemical Regulation. Session chair University of Otago, 5/2/2003, Dunedin, New Zealand. Invited
talk: Mechanisms of biochemical regulation. American Physical Society meeting, 3/2/2003, Austin TX, Invited
tutorial: Transcriptional Regulatory Networks: Data, Analysis and
Modeling EBI seminar series, 12/9/2002, European Bioinformatics
Institute, Hinxton, UK, seminar: Mechanisms associated with cGMP
binding and activation of cGMP-dependent protein kinase LANL workshop on enabling concepts in systems biology, 9/19/2002,
Santa Fe. Invited talk: Integrating systems and structural biology:
structural mechanisms in cGMP binding and activation of cGMP-dependent
protein kinase CNLS seminar series, Processes of Life, from the Molecule to the
Cell, 2/19/2002, Los Alamos National Lab, Los Alamos, NM, seminar:
Large-Scale Shape Changes in cGMP-dependent Protein Kinase American Chemical Society Rocky Mountain Regional Meeting,
10/14/2002, Albuquerque. Invited talk: Mechanisms associated with cGMP
binding and activation of cGMP-dependent protein kinase NCGR Friday seminar series, 12/7/2001, National Center for Genome
Resources, Santa Fe, NM, seminar: A Biosystems Modeling Project, with
John Ambrosiano (CCS-1) APS User Meeting, 10/9/2001, Argonne National Laboratory,
Argonne, IL, invited talk: Diffuse Scattering: Methods for Molecular
Structure and Dynamics LANL/UCSD workshop for exploring collaborations,
9/8/2001-9/9/2001, San Diego, CA, invited talk: Diffuse Scattering and
Database Methods National Center for Genome Resources, March 2001, Santa Fe NM,
seminar: Singular value decomposition analysis of microarray data TIGR’s Fourth
Annual Conference on Computational Genomics, November 2000, Baltimore
MD, talk: Validadtion of singular value decomposition of global
expression data (Dyck et al reference above) Gordon Research
Conference on Diffraction Methods in Molecular Biology, Summer 2000,
Andover NH, invited talk: Harnessing the potential of a structure
database Los Alamos
Bioscience Postdoctoral Forum, June 2000, Los Alamos, NM, talk:
Regulation of muscle contraction: a molecular model of the interaction
between troponin-I and troponin-C Biophysical
Society Meeting, February 2000, New Orleans, LA, poster: A molecular
model of the troponin-C/troponin-I interaction (reference above) Quantitative
Challenges in the Post-Genomic Era, La Jolla Interfaces in Science
2000, January 2000, San Diego, CA, poster: A molecular model of the
troponin-C/troponin-I interaction Integrated
Structural Biology Resource, November 1999, Los Alamos National
Laboratory, Los Alamos, NM, seminar: Getting tense: a molecular model
of the troponin-C/troponin-I interaction Los Alamos
National Laboratory, February 1999, Los Alamos, NM, invited talk:
Refinement of X-ray structures using a database of pairwise interatomic
distance probabilities School of
Biological Sciences, December 1998, Auckland University, Auckland, New
Zealand, invited talk: Dynamics in Calmodulin Department of
Chemistry, December 1998, Massey University, Palmerston North, New
Zealand, invited talk: Dynamics in Calmodulin Department of
Biochemistry, December 1998, Otago University, Dunedin, New Zealand,
invited talk: Dynamics in Calmodulin Gordon Research
Conference on Diffraction Methods in Molecular Biology, Summer 1998,
Andover, NH, invited talk: Making sense of diffuse scattering and
making use of all the X-rays Parke-Davis
Pharmaceuticals, Spring 1998, Ann Arbor, MI, invited talk: Dynamics in
calmodulin crystals Parke-Davis
Pharmaceuticals, Spring 1998, Ann Arbor, MI, invited talk: Refinement
of X-ray structures using a database of pairwise interatomic distance
probabilities Biophysical
Society Meeting, Winter 1998, Kansas City, MO, invited talk: Refinement
of X-ray structures using a database of pairwise atomic distance
probabilities (reference above) Computational
Biomedicine Symposium, Fall 1997, Baylor College of Medicine, Houston,
TX, poster: Refinement of X-ray structures using a database of pairwise
atomic distance probabilities Department of
Molecular and Cellular Biology, Fall 1997, Brown University,
Providence, RI, invited talk: Dynamics in calmodulin crystals Department of
Biochemistry and Cell Biology, Fall 1997, Rice University, Houston, TX,
seminar: Dynamics in calmodulin crystals Keck Center
Annual Research Conference on Computational Biology, Fall 1997,
Galveston, TX, Dunn Prize poster on motions of calmodulin Biophysical
Society Meeting, Winter 1997, New Orleans, LA, poster on preliminary
results of motions of calmodulin (reference above) ASBMB
Computational Biology Symposium, Fall 1996, Whistler, BC, Canada,
poster on diffuse X-ray scattering from calmodulin Keck Center
Annual Research Conference on Computational Biology, Fall 1996,
Galveston, TX, poster on wavelet decomposition of X-ray diffraction
images International
Union of Crystallography Meeting, August 1996, Seattle, WA, invited
talk on dissertation research CHESS Journal
Club, May 1996, Cornell High-Energy Synchrotron Source, Ithaca, NY,
invited talk on dissertation research Biophysical
Society Meeting, Winter 1996, Washington, DC, poster on dissertation
research (reference above) Keck Center for
Computational Biology Colloquium, September 1995, Rice University,
Houston, TX, invited talk on dissertation research DCRT Structural
Biology Division, 1994, National Institutes of Health, Bethesda, MD,
invited talk on dissertation research
Last modified Thursday, 04-Jun-2009 12:38:30 MDT
Michael Wall / mewall@lanl.gov
Los Alamos National Laboratory,
CCS-3 MS B256,
Los Alamos NM 87545
tel: 505.665.4209 / fax: 505.667.1126